[2024-01-24 11:51:11,250] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,257] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,259] [INFO] DQC Reference Directory: /var/lib/cwl/stged38992a-9588-4a31-9631-8eac8a075c39/dqc_reference
[2024-01-24 11:51:12,668] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,669] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,669] [INFO] Running command: gunzip -c /var/lib/cwl/stg24736857-751f-45c6-8408-f841b3b2639a/GCF_006443095.1_ASM644309v1_genomic.fna.gz | prodigal -d GCF_006443095.1_ASM644309v1_genomic.fna/cds.fna -a GCF_006443095.1_ASM644309v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:32,205] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:32,206] [INFO] Task started: HMMsearch
[2024-01-24 11:51:32,206] [INFO] Running command: hmmsearch --tblout GCF_006443095.1_ASM644309v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged38992a-9588-4a31-9631-8eac8a075c39/dqc_reference/reference_markers.hmm GCF_006443095.1_ASM644309v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:32,556] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:32,558] [INFO] Found 6/6 markers.
[2024-01-24 11:51:32,604] [INFO] Query marker FASTA was written to GCF_006443095.1_ASM644309v1_genomic.fna/markers.fasta
[2024-01-24 11:51:32,605] [INFO] Task started: Blastn
[2024-01-24 11:51:32,605] [INFO] Running command: blastn -query GCF_006443095.1_ASM644309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged38992a-9588-4a31-9631-8eac8a075c39/dqc_reference/reference_markers.fasta -out GCF_006443095.1_ASM644309v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:33,270] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:33,276] [INFO] Selected 22 target genomes.
[2024-01-24 11:51:33,276] [INFO] Target genome list was writen to GCF_006443095.1_ASM644309v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:33,287] [INFO] Task started: fastANI
[2024-01-24 11:51:33,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg24736857-751f-45c6-8408-f841b3b2639a/GCF_006443095.1_ASM644309v1_genomic.fna.gz --refList GCF_006443095.1_ASM644309v1_genomic.fna/target_genomes.txt --output GCF_006443095.1_ASM644309v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:52,080] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:52,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged38992a-9588-4a31-9631-8eac8a075c39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:52,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged38992a-9588-4a31-9631-8eac8a075c39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:52,100] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:52,100] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:52,100] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Aquimarina algicola	strain=M625	GCA_006443095.1	2589995	2589995	type	True	100.0	1950	1951	95	conclusive
Aquimarina mytili	strain=KCTC 23302	GCA_016735115.1	874423	874423	type	True	78.2621	518	1951	95	below_threshold
Aquimarina megaterium	strain=XH134	GCA_000520975.1	1443666	1443666	type	True	78.2574	554	1951	95	below_threshold
Aquimarina longa	strain=SW024	GCA_001401755.1	1080221	1080221	type	True	78.2185	491	1951	95	below_threshold
Aquimarina spongiae	strain=DSM 22623	GCA_900141785.1	570521	570521	type	True	78.2125	465	1951	95	below_threshold
Aquimarina atlantica	strain=22II-S11-z7	GCA_000626715.1	1317122	1317122	type	True	78.1933	530	1951	95	below_threshold
Aquimarina latercula	strain=DSM 2041	GCA_000430645.1	987	987	type	True	78.1681	456	1951	95	below_threshold
Aquimarina macrocephali	strain=JAMB N27	GCA_000520995.1	666563	666563	type	True	78.1551	518	1951	95	below_threshold
Aquimarina sediminis	strain=w01	GCA_002895435.1	2070536	2070536	type	True	78.0907	480	1951	95	below_threshold
Aquimarina aggregata	strain=RZW4-3-2	GCA_001632745.1	1642818	1642818	type	True	77.7808	544	1951	95	below_threshold
Aquimarina amphilecti	strain=DSM 25232	GCA_900109375.1	1038014	1038014	type	True	77.5517	424	1951	95	below_threshold
Aquimarina brevivitae	strain=DSM 17196	GCA_004216895.1	323412	323412	type	True	77.14	221	1951	95	below_threshold
Mesonia mobilis	strain=KCTC 12708	GCA_014651475.1	369791	369791	type	True	76.5795	91	1951	95	below_threshold
Mesonia mobilis	strain=DSM 19841	GCA_000423405.1	369791	369791	type	True	76.54	93	1951	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.415	99	1951	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.2883	69	1951	95	below_threshold
Seonamhaeicola aphaedonensis	strain=CECT 8487	GCA_003386195.1	1461338	1461338	type	True	76.1942	105	1951	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.1437	111	1951	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	76.025	119	1951	95	below_threshold
Wenyingzhuangia heitensis	strain=DSM 101599	GCA_011762155.1	1487859	1487859	type	True	75.8935	88	1951	95	below_threshold
Flavobacterium oreochromis	strain=Costa Rica 04-02-TN	GCA_019565455.1	2906078	2906078	type	True	75.8839	87	1951	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	75.6966	134	1951	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:52,102] [INFO] DFAST Taxonomy check result was written to GCF_006443095.1_ASM644309v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:52,103] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:52,103] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:52,104] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged38992a-9588-4a31-9631-8eac8a075c39/dqc_reference/checkm_data
[2024-01-24 11:51:52,105] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:52,163] [INFO] Task started: CheckM
[2024-01-24 11:51:52,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006443095.1_ASM644309v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006443095.1_ASM644309v1_genomic.fna/checkm_input GCF_006443095.1_ASM644309v1_genomic.fna/checkm_result
[2024-01-24 11:52:45,671] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:45,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:45,693] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:45,693] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:45,693] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006443095.1_ASM644309v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:45,694] [INFO] Task started: Blastn
[2024-01-24 11:52:45,694] [INFO] Running command: blastn -query GCF_006443095.1_ASM644309v1_genomic.fna/markers.fasta -db /var/lib/cwl/stged38992a-9588-4a31-9631-8eac8a075c39/dqc_reference/reference_markers_gtdb.fasta -out GCF_006443095.1_ASM644309v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:46,532] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:46,535] [INFO] Selected 17 target genomes.
[2024-01-24 11:52:46,535] [INFO] Target genome list was writen to GCF_006443095.1_ASM644309v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:46,546] [INFO] Task started: fastANI
[2024-01-24 11:52:46,546] [INFO] Running command: fastANI --query /var/lib/cwl/stg24736857-751f-45c6-8408-f841b3b2639a/GCF_006443095.1_ASM644309v1_genomic.fna.gz --refList GCF_006443095.1_ASM644309v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006443095.1_ASM644309v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:02,941] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:02,955] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:02,955] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_006443095.1	s__Aquimarina sp006443095	100.0	1950	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007489275.1	s__Aquimarina algiphila	78.5944	628	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.78	98.78	0.88	0.88	2	-
GCF_900312745.1	s__Aquimarina sp900312745	78.3296	513	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.61	95.54	0.91	0.91	4	-
GCF_000520975.1	s__Aquimarina megaterium	78.2575	554	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.79	98.77	0.92	0.92	4	-
GCF_001401755.1	s__Aquimarina longa	78.2268	490	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141785.1	s__Aquimarina spongiae	78.2256	463	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000626715.1	s__Aquimarina atlantica	78.1863	531	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000430645.1	s__Aquimarina latercula	78.1656	457	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.44	98.41	0.94	0.92	4	-
GCF_900299535.1	s__Aquimarina sp900299535	78.1211	476	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	95.11	95.11	0.81	0.81	2	-
GCF_900312815.1	s__Aquimarina sp900312815	78.1017	479	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002895435.1	s__Aquimarina sediminis	78.0886	481	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900299505.1	s__Aquimarina sp900299505	77.796	422	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001632745.1	s__Aquimarina aggregata	77.7903	542	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	98.64	98.63	0.93	0.92	3	-
GCF_018100805.1	s__Aquimarina sp018100805	77.7888	435	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017897595.1	s__Aquimarina sp017897595	77.5398	364	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003443675.1	s__Aquimarina sp003443675	77.4747	422	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000423405.1	s__Mesonia mobilis	76.5213	95	1951	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:02,957] [INFO] GTDB search result was written to GCF_006443095.1_ASM644309v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:02,958] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:02,962] [INFO] DFAST_QC result json was written to GCF_006443095.1_ASM644309v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:02,962] [INFO] DFAST_QC completed!
[2024-01-24 11:53:02,962] [INFO] Total running time: 0h1m52s